Probably the cleanest examples of where visualization makes things very clear is explaining the groupoid structure of paths [1], and how to generate lattice quivers [2].
But I also enjoy some of the aesthetic qualities of the sections on coverings [3] (intricate), vertex colorings [4] (very colorful!), toroidal lattices [5], and products of quivers [6]. The last in particular involves trying to understand products from both an algebraic and geometric perspective, and 3D visualization is especially helpful there, giving intuition for how a certain product slices off hexagonal pieces of a hypercube.
[1] https://quivergeometry.net/qg/paths/
[2] https://quivergeometry.net/qg/lattice-quivers/
[3] https://quivergeometry.net/qg/covers/
[4] https://quivergeometry.net/qg/colorings/